21st International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology |
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causing infections in humans is genetically indistinguishable from the virus found in Arabian camels (dromedaries) in the Middle East. Although no primary human case of MERS was reported outside the Arabian Peninsula, camel populations in Africa are known to have high prevalence of antibodies against MERS-CoV. We carried out surveillance for MERS-CoV in dromedaries in Africa and Central Asia. By MERS-CoV spike pseudoparticle neutralization assay we confirmed that camel serum samples from African countries have high prevalence of MERS-CoV antibodies. Using RT-qPCR we detected MERS-CoV positives in camel nasal swabs from all different African countries from which samples were collected. However, dromedary serum and swab samples from Kazakhstan in Central Asia were negative for MERS-CoV by these assays. Phylogenetic analysis of the spike gene revealed that MERS-CoVs from Africa formed a cluster closely related to but distinct from the viruses from the Arabian Peninsula. Results from this study suggest that MERS-CoV is actively circulating in dromedary populations in Africa and the virus in Africa is phylogenetically distinct from that in the Middle East. A47 Origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china: phylogenetics and coalescence analysis Yanqun Wang,1 Di Liu,2,3 Weifeng Shi,4 Roujian Lu,1 Wenling Wang,1 Yanjie Zhao,1 Yao Deng,1 Weimin Zhou,1 Hongguang Ren,5 Jun Wu,2 Yu Wang,6 Guizhen Wu,1 George F. Gao,1,2,6 Wenjie Tan,1 1
Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention, Beijing, China, 2CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, China, 3 Network Information Center Institute of Microbiology Chinese Academy of Sciences, Beijing, China, 4Institute of Pathogen Biology Taishan Medical College, Taian, China, 5State Key Laboratory of Pathogen and Biosecurity, Beijing, China and 6Office of DirectorGeneral Chinese Center for Disease Control and Prevention, Beijing, China
The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. A48 Inference of biological functionality in individual genomic secondary structural elements found within capulavirus genomes P. Hartnady,1,* D. Martin,1 B. Muhire,1 P. Roumagnac,2 1
UCT Faculty Of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Cape Town and 2Cirad, France
The seeming simplicity of the iconic DNA double helix is deceptive. The genomes of single-stranded DNA and RNA viruses
S17
often contain numerous nucleic acid secondary structures. Whilst a number of these secondary structural elements have been found to play crucial roles during the life cycles of these viruses, the majority have neither any identified function nor known impact on viral fitness and evolution. Secondary structures can be predicted using nearest neighbour free-energy parameters that quantify the stability of a given secondary structure. Using an array of bioinformatic techniques we investigated the influence of inferred secondary structures on the sequence evolution of capulaviruses, a diverse genera of single stranded DNA viruses. We detected a significant association between structured regions of the genome and selective constraints on synonymous substitutions in coding regions. This is suggestive of either natural selection acting to preserve these structures or a predisposition toward lower mutation rates in base-paired regions of the genome. In addition, coevolution analyses revealed a significant tendency for nucleotides that are base-paired in predicted structures to coevolve in a complementary manner. Combined, these results highlight the pervasiveness of conserved genomic secondary structures within capulavirus genomes and support the notion that natural selection is favouring the maintenance of these structures, providing compelling evidence of their likely biological relevance. This structure-first strategy for comparative analysis of genomewide secondary structures can be broadly applied to understand the contributions of higher-order genome structures to viral replication and pathogenicity. A49 Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya James R. Otieno, 1,* Charles N. Agoti,1,2 Caroline W. Gitahi,1 Ann Bett,1 Mwanajuma Ngama,1 Graham F. Medley,3 Patricia A. Cane,4 D. James Nokes,1,5 1
Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) – Wellcome Trust Research Programme, Kilifi, Kenya, 2Department of Biomedical Sciences, Pwani University, Kilifi, Kenya, 3Department of Global Health & Development London School of Hygiene and Tropical Medicine, London, UK, 4Public Health England, Salisbury, UK and 5School of Life Sciences and WIDER, University of Warwick, Coventry, UK
The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing efficiency of pre-existing immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000–12) in Kilifi (n ¼ 649), Kenya, and contemporaneous sequences (n ¼ 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2, then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3.58 103 [95% HPD: 3.04–4.16] nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causing infections in humans is genetically indistinguishable from the virus found in Arabian camels (dromedaries) in the Middle East. Although no primary human case of MERS was reported outside the Arabian Peninsula, camel populations in Africa are known to have high prevalence of antibodies against MERS-CoV. We carried out surveillance for MERS-CoV in dromedaries in Africa and Central Asia. By MERS-CoV spike pseudoparticle neutralization assay we confirmed that camel serum samples from African countries have high prevalence of MERS-CoV antibodies. Using RT-qPCR we detected MERS-CoV positives in camel nasal swabs from all different African countries from which samples were collected. However, dromedary serum and swab samples from Kazakhstan in Central Asia were negative for MERS-CoV by these assays. Phylogenetic analysis of the spike gene revealed that MERS-CoVs from Africa formed a cluster closely related to but distinct from the viruses from the Arabian Peninsula. Results from this study suggest that MERS-CoV is actively circulating in dromedary populations in Africa and the virus in Africa is phylogenetically distinct from that in the Middle East. A47 Origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china: phylogenetics and coalescence analysis Yanqun Wang,1 Di Liu,2,3 Weifeng Shi,4 Roujian Lu,1 Wenling Wang,1 Yanjie Zhao,1 Yao Deng,1 Weimin Zhou,1 Hongguang Ren,5 Jun Wu,2 Yu Wang,6 Guizhen Wu,1 George F. Gao,1,2,6 Wenjie Tan,1 1
Key Laboratory of Medical Virology Ministry of Health, National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention, Beijing, China, 2CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology Chinese Academy of Sciences, Beijing, China, 3 Network Information Center Institute of Microbiology Chinese Academy of Sciences, Beijing, China, 4Institute of Pathogen Biology Taishan Medical College, Taian, China, 5State Key Laboratory of Pathogen and Biosecurity, Beijing, China and 6Office of DirectorGeneral Chinese Center for Disease Control and Prevention, Beijing, China
The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus. A48 Inference of biological functionality in individual genomic secondary structural elements found within capulavirus genomes P. Hartnady,1,* D. Martin,1 B. Muhire,1 P. Roumagnac,2 1
UCT Faculty Of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Cape Town and 2Cirad, France
The seeming simplicity of the iconic DNA double helix is deceptive. The genomes of single-stranded DNA and RNA viruses
S17
often contain numerous nucleic acid secondary structures. Whilst a number of these secondary structural elements have been found to play crucial roles during the life cycles of these viruses, the majority have neither any identified function nor known impact on viral fitness and evolution. Secondary structures can be predicted using nearest neighbour free-energy parameters that quantify the stability of a given secondary structure. Using an array of bioinformatic techniques we investigated the influence of inferred secondary structures on the sequence evolution of capulaviruses, a diverse genera of single stranded DNA viruses. We detected a significant association between structured regions of the genome and selective constraints on synonymous substitutions in coding regions. This is suggestive of either natural selection acting to preserve these structures or a predisposition toward lower mutation rates in base-paired regions of the genome. In addition, coevolution analyses revealed a significant tendency for nucleotides that are base-paired in predicted structures to coevolve in a complementary manner. Combined, these results highlight the pervasiveness of conserved genomic secondary structures within capulavirus genomes and support the notion that natural selection is favouring the maintenance of these structures, providing compelling evidence of their likely biological relevance. This structure-first strategy for comparative analysis of genomewide secondary structures can be broadly applied to understand the contributions of higher-order genome structures to viral replication and pathogenicity. A49 Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya James R. Otieno, 1,* Charles N. Agoti,1,2 Caroline W. Gitahi,1 Ann Bett,1 Mwanajuma Ngama,1 Graham F. Medley,3 Patricia A. Cane,4 D. James Nokes,1,5 1
Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) – Wellcome Trust Research Programme, Kilifi, Kenya, 2Department of Biomedical Sciences, Pwani University, Kilifi, Kenya, 3Department of Global Health & Development London School of Hygiene and Tropical Medicine, London, UK, 4Public Health England, Salisbury, UK and 5School of Life Sciences and WIDER, University of Warwick, Coventry, UK
The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing efficiency of pre-existing immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000–12) in Kilifi (n ¼ 649), Kenya, and contemporaneous sequences (n ¼ 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2, then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi dataset was estimated at 3.58 103 [95% HPD: 3.04–4.16] nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European
